title: CryoEM and molecular dynamics of the circadian KaiB-KaiC complex indicates that KaiB monomers interact with KaiC and block ATP binding clefts.
abstract: The circadian control of cellular processes in cyanobacteria is regulated by a posttranslational oscillator formed by three Kai proteins. During the oscillator cycle, KaiA serves to promote autophosphorylation of KaiC while KaiB counteracts this effect. Here, we present a crystallographic structure of the wild-type Synechococcus elongatus KaiB and a cryo-electron microscopy (cryoEM) structure of a KaiBC complex. The crystal structure shows the expected dimer core structure and significant conformational variations of the KaiB C-terminal region, which is functionally important in maintaining rhythmicity. The KaiBC sample was formed with a C-terminally truncated form of KaiC, KaiC-Δ489, which is persistently phosphorylated. The KaiB-KaiC-Δ489 structure reveals that the KaiC hexamer can bind six monomers of KaiB, which form a continuous ring of density in the KaiBC complex. We performed cryoEM-guided molecular dynamics flexible fitting simulations with crystal structures of KaiB and KaiC to probe the KaiBC protein-protein interface. This analysis indicated a favorable binding mode for the KaiB monomer on the CII end of KaiC, involving two adjacent KaiC subunits and spanning an ATP binding cleft. A KaiC mutation, R468C, which has been shown to affect the affinity of KaiB for KaiC and lengthen the period in a bioluminescence rhythm assay, is found within the middle of the predicted KaiBC interface. The proposed KaiB binding mode blocks access to the ATP binding cleft in the CII ring of KaiC, which provides insight into how KaiB might influence the phosphorylation status of KaiC.
authors.affiliation: Department of Pharmacology and Cleveland Center for Membrane and Structural Biology, Case Western Reserve University, Cleveland, OH 44106, USA.
authors.forename: Seth A
authors.initials: SA
authors.lastname: Villarreal
authors.forename: Rekha
authors.initials: R
authors.lastname: Pattanayek
authors.forename: Dewight R
authors.initials: DR
authors.lastname: Williams
authors.forename: Tetsuya
authors.initials: T
authors.lastname: Mori
authors.forename: Ximing
authors.initials: X
authors.lastname: Qin
authors.forename: Carl H
authors.initials: CH
authors.lastname: Johnson
authors.forename: Martin
authors.initials: M
authors.lastname: Egli
authors.forename: Phoebe L
authors.initials: PL
authors.lastname: Stewart
mesh_terms: D000255:Adenosine Triphosphate / Q000378:metabolism*; D001426:Bacterial Proteins / Q000037:antagonists & inhibitors / Q000737:chemistry / Q000378:metabolism*; D001665:Binding Sites / Q000502:physiology; D056925:Circadian Rhythm Signaling Peptides and Proteins / Q000037:antagonists & inhibitors / Q000737:chemistry / Q000378:metabolism*; D020285:Cryoelectron Microscopy; D018360:Crystallography, X-Ray; D008958:Models, Molecular; D056004:Molecular Dynamics Simulation; D046912:Multiprotein Complexes / Q000737:chemistry; D010766:Phosphorylation; D011485:Protein Binding; D055503:Protein Multimerization / Q000502:physiology; D020836:Protein Structure, Quaternary; D046940:Synechococcus / Q000235:genetics / Q000378:metabolism*
chemical_list: D001426:Bacterial Proteins; D056925:Circadian Rhythm Signaling Peptides and Proteins; C114270:KaiB protein, cyanobacteria; C114271:KaiC protein, cyanobacteria; D046912:Multiprotein Complexes; D000255:Adenosine Triphosphate
keywords: EM; FSC; Fourier shell correlation; GST; MDFF; PDB; PTO; Protein Data Bank; SAXS; Synechococcus elongatus; circadian oscillator; cryo-electron microscopy; cryoEM; electron microscopy; glutathione S-transferase; molecular dynamics flexible fitting; posttranslational oscillator; protein–protein interface; small-angle X-ray scattering